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Crystal structure of cbmbc (family CBM26) from eubacterium rectale AMY13K in complex with maltoheptaose
Analyse Crystal structure of cbmbc (family CBM26) from eubacterium rectale AMY13K in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B3P
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMY13K
- UniProt
- D4JJZ5
- Ligands
- GLC
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 0% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | AMY13K | protein | 209 | 0% helix, 42% strand | D4JJZ5 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 14 copies · chains A, B
- FMT · Formic acid · additive · 19 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.73 | 0.79 | 51 | FMT |
| 2 | 218 | 0.51 | 0.76 | 36 | FMT |
| 3 | 87 | 0.43 | 0.80 | 21 | empty |
| 4 | 125 | 0.41 | 0.75 | 19 | EDO, FMT |
| 5 | 59 | 0.29 | 0.75 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6B3P · Crystal structure of CBMbc (family CBM26) from Eubacterium rectale Amy13K in Complex with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt D4JJZ5
- Elsewhere: RCSB PDB 6B3P · PDBe 6B3P · UniProt D4JJZ5
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